Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate Echvi_3219 Echvi_3219 Zn-dependent alcohol dehydrogenases
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__Cola:Echvi_3219 Length = 343 Score = 200 bits (509), Expect = 4e-56 Identities = 114/327 (34%), Positives = 179/327 (54%), Gaps = 13/327 (3%) Query: 33 RATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTT-YPIVPGHEIVGVVTEVGSKVEKVKVG 91 +A E + ++V+ GVCH+D H +W P++PGHE +G V VGS V+ K G Sbjct: 26 KAPNENQILVQVMASGVCHTDLHAADGDWPVKPRLPLIPGHEGIGYVAAVGSNVKNTKEG 85 Query: 92 DNVGIGCLVGSCRSCESCCDNRESHCENTIDTYGSIYFDGTMTHGGYSDTMVADEHFILR 151 D VG+ L +C CE C E+ CE+ ++ G GGY++ ++AD +++ R Sbjct: 86 DIVGVPWLYSACGHCEHCITGWETLCESQVN-------GGYSVDGGYAEYVLADPNYVGR 138 Query: 152 WPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGLGGLGHVAVKMAKAFGAQVT 211 + + AP+LCAG+T Y LK + +PG + + G+GGLGHVAV+ AKA G V Sbjct: 139 FSGAIDFVQMAPILCAGVTVYKGLKETEV-RPGQWVAISGIGGLGHVAVQYAKAMGLHVL 197 Query: 212 VIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDGIIDT-VPVNHPLA--PLFDLL 268 +D+S+ K A +KLGAD + + +++ AR G+ V P+A DLL Sbjct: 198 AVDVSDDKLNLA-KKLGADRVVNGKNPDEVMNARKETGGVHGVLVTAVSPVAFRQALDLL 256 Query: 269 KPNGKLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQEMLDFAAKHNITADVEVI 328 + G LVM G P F+LP+F + R + G+I G K+ QE +DFA + +T V+ Sbjct: 257 RRKGTLVMNGLPPGSFDLPIFETVLNRYTVRGSIVGTRKDLQEAIDFAMEGKVTTTVKSA 316 Query: 329 PMDYVNTAMERLVKSDVRYRFVIDIAN 355 P++ +N +++ K + R V+DI + Sbjct: 317 PLEDINLIFDQMKKGQIEGRMVLDIGH 343 Lambda K H 0.319 0.137 0.415 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 295 Number of extensions: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 365 Length of database: 343 Length adjustment: 29 Effective length of query: 336 Effective length of database: 314 Effective search space: 105504 Effective search space used: 105504 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory